6LA4: Full echovirus 11 particle at pH 5.5

Name: PDB 6LA4: Cryo-EM structure of full echovirus 11 particle at pH 5.5
Published: 2020-10-07
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Cryo-EM structure of full echovirus 11 particle at pH 5.5. Determined by electron microscopy at 2.34 Å resolution. Released 7 Oct 2020.

Method: Electron microscopy
Resolution: 2.34 Å
Organism: Echovirus E11
Chains: 4
Atoms: 6,536
Mol. weight: 94.1 kDa
Ligands: SPH
Released: 7 Oct 2020

Explore 6LA4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6LA4 contains 33 α-helices and 67 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 12 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	13	1	2
α-helix	14-16	3
β-strand	17	1	3
α-helix	18-19	2
β-strand	20	1	4
β-strand	31-32	2	5
α-helix	34-36	3
α-helix	44-46	3
β-strand	50	1	4
β-strand	53	1	3
β-strand	58	1	2
β-strand	63	1	6
α-helix	64-68	5
β-strand	72-80	9	7
β-strand	90-94	5	8
α-helix	101-107	7
β-strand	110-127	18	7
α-helix	138-140	3
β-strand	141-147	7	8
α-helix	160-163	4
β-strand	169-173	5	8
α-helix	177-179	3
β-strand	180-183	4	7
β-strand	192-193	2	7
β-strand	198	1	9
β-strand	199	1	10
β-strand	208	1	10
α-helix	210-212	3
β-strand	218-223	6	8
β-strand	232-250	19	7
α-helix	252-254	3
α-helix	257-258	2
β-strand	275	1	11

Chain B: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	14-18	5	12
β-strand	21-25	5	12
β-strand	28	1	13
β-strand	32-33	2	13
α-helix	41-43	3
α-helix	44-46	3
α-helix	52-53	2
β-strand	54	1	13
β-strand	64-65	2	13
β-strand	69-70	2	14
β-strand	78-82	5	15
α-helix	90-98	9
β-strand	99-111	13	13
β-strand	119-128	10	15
β-strand	134	1	16
α-helix	143-146	4
β-strand	148	1	17
β-strand	151	1	17
α-helix	152	1
β-strand	153-154	2	15
β-strand	156	1	18
β-strand	166	1	16
β-strand	169	1	18
α-helix	170-172	3
α-helix	179-184	6
β-strand	187-191	5	15
β-strand	197-202	6	13
β-strand	211	1	13
β-strand	216	1	9
β-strand	219-230	12	15
β-strand	240-241	2	14
β-strand	242-255	14	13
α-helix	258-259	2

Chain C: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	23	1	7
α-helix	30-33	4
β-strand	39-40	2	7
β-strand	42	1	6
α-helix	44-47	4
β-strand	51-52	2	5
β-strand	58	1	11
α-helix	65-68	4
α-helix	69	1
β-strand	70-72	3	5
β-strand	81-86	6	19
α-helix	99-104	6
β-strand	107-111	5	20
β-strand	114-120	7	5
β-strand	127	1	21
β-strand	129-135	7	19
α-helix	140-142	3
α-helix	145-148	4
β-strand	152-157	6	19
β-strand	163-168	6	5
β-strand	177-178	2	20
β-strand	189-194	6	19
β-strand	199	1	21
β-strand	208-216	9	5
β-strand	221-225	5	20

Chain D: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
α-helix	8-9	2
β-strand	26-29	4	1
α-helix	36-38	3
α-helix	40-41	2
α-helix	51-54	4
β-strand	57	1	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Capsid protein VP1	A	protein	285	Echovirus E11	Q2LJ73
Capsid protein VP2	B	protein	251	Echovirus E11	A0A0R5YS56
Capsid protein VP3	C	protein	238	Echovirus E11	A0A346I7K2
Capsid protein VP4	D	protein	69	Echovirus E11	E0WN77

Sequence of entity 1 (A), FASTA

>6LA4_1 Capsid protein VP1 (chains A)
VVEAVENAVARVADTISSGPSNSQAVPALTAVETGHTSQVTPSDTIQTRHVRNYHSRSES
SIENFLCRSACVYMGEYHTTNTDTSKLFASWTINARRMVQMRRKLELFTYVRFDMEVTFV
ITSKQDQGTQLGQDMPPLTHQIMYIPPGGPIPKSVTDYTWQTSTNPSIFWTEGNAPPRMS
IPFISIGNAYSNFYDGWSHFSQNGVYGYNTLNHMGQIYVRHVNGSSPLPMTSTVRMYFKP
KHVKVWVPRPPRLCQYKNASTVNFTPTNITEKRQSINYIPETVKP

Sequence of entity 2 (B), FASTA

>6LA4_2 Capsid protein VP2 (chains B)
DRVRSITLGNSTITTQESANVVVAYGRWPEYLKDNEATAEDQPTQPDVATCRFYTLESVT
WERDSPGWWWKFPDALKDMGLFGQNMYYHYLGRAGYTIHVQCNASKFHQGCLMVVCVPEA
EMGCSQVDGTVNEHSLSEGETAKKFASTSTNGTNTVQSIVTNAGMGVGVGNLTIFPHQWI
NLRTNNCATIVMPYINNVPMDNMFRHHNFTLMIIPFVPLDYSSDSSTYVPITVTVAPMCA
EYNGLRLATSL

Sequence of entity 3 (C), FASTA

>6LA4_3 Capsid protein VP3 (chains C)
GLPVMNTPGSNQFLTSDDFQSPSAMPQFDVTPELNIPGEVQNLMEIAEVDSVVPVNNVEG
KLDTMEIYRIPVQSGNHQSSQVFGFQVQPGLDNVFKHTLLGEILNYYAHWSGSIKLTFVF
CGSAMATGKFLLAYAPPGANAPKSRKDAMLGTHIIWDVGLQSSCVLCIPWISQTHYRLVQ
QDEYTSAGNVTCWYQTGIVVPAGTPTSCSIMCFVSACNDFSVRLLKDTPFIEQSALLQ

Sequence of entity 4 (D), FASTA

>6LA4_4 Capsid protein VP4 (chains D)
MGAQVSTQKTGAHETGLNASGRSIIHYTNINYYKDAASNSANRQDFSQDPGKFTEPVKDI
MVKSLPALN

Ligands and cofactors

ID	Name	Formula	Copies
SPH	Sphingosine	C18 H37 N O2	1

Primary citation

Molecular and structural basis of Echovirus 11 infection by using the dual-receptor system of CD55 and FcRn. Niu, S., Liu, C., Liu, C. et al. Chin Sci Bull (2020). DOI 10.1360/TB-2019-0786

Other PDB entries of the same protein (UniProt Q2LJ73), best resolution first:

6LA3 2.32 Å, Cryo-EM structure of full echovirus 11 particle at pH 7.4
6LA6 2.39 Å, Cryo-EM structure of echovirus 11 complexed with its uncoating receptor FcRn at pH 7.4
6LAP 2.49 Å, Cryo-EM structure of echovirus 11 A-particle at pH 7.4
6LB1 2.58 Å, Cryo-EM structure of echovirus 11 A-particle at pH 5.5
6LBQ 2.6 Å, Cryo-EM structure of echovirus 11 empty particle at pH 5.5
6LAO 2.64 Å, Cryo-EM structure of echovirus 11 complexed with its attaching receptor CD55 at pH 5.5
6LA7 2.82 Å, Cryo-EM structure of echovirus 11 complexed with its uncoating receptor FcRn at pH 5.5
6LA5 2.86 Å, Cryo-EM structure of echovirus 11 complexed with its attaching receptor CD55 at pH 7.4
6LBO 3.18 Å, Cryo-EM structure of echovirus 11 empty particle at pH 7.4

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